Sequence
atgc intronic sequence ATGC exonic sequence...cgattcattagctcccgaagactaagaggatttgtggacttagaagccagcttgatgatccatggatctctgattattcagtgttgatgttatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39660.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G14850.1 (Glycine max), 3'ss of exon 1
-cgattcat-tagctcccgaagac------taagaggatttgtggacttagaagccagcttgatgatccatggatctctgattattcagtgttgatgttatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
| |||| ||| || | | ||||||| | || ||| | || | || || | ||||| | | |||| |||| |||| || ||||| |||||||||||||| || |||||||||| ||||| ||||| || || ||||| ||||| || ||||| ||||| || ||||| || |
gaaaatcatatagtcccttgatgtctctttttcattgatttgtttatttc-aagtaattatgccttgcaattgaggtgtgatt--caaattttga----atgt-atagCTGAATATCGTGGAAGGGAAGATGCAATATCTGTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGGATAGTTACTGTTTCTTGCGGACATT
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 1
cgattcat-tagctcccgaagac------taagaggatttgtggacttagaagccagcttgatgatccatggatctctgattattcagtgttgatgttatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
| |||| ||| || | | ||||| | ||| | || || ||| | ||||| | | |||| | ||| | |||| || ||||| |||||||||||||| || | |||||||| ||||| ||||| || || ||||| ||||| |||||||| ||||| || ||||| || |
--aatcatatagtcccttcatgtctctttttcatcattttgtttatttaagaaattatgccttg--taattgatgtgtgatt--caaattttgaatgtgtgt-gtagCTGAATATCGTGGAAGGGAAGATGCAATATCTTTATGATGATAGTGGGAGGCGTTACCTTGATGCATTTGCGGGAATAGTTACTGTTTCTTGCGGACATT
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 1
---------cgattcattagctcccgaagactaagaggatttgtggact-tagaagccagcttgatgatccatggatctctgattattcagtgttgatgttatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
| | | | || || |||| ||| || | | ||| | | || ||| | || | | || || | ||| |||||| |||| ||||| || || || |||||||| || | | ||||||| ||||||||| ||||| ||||| |||||||||||||| ||| | || || || || |
gttaaaaagtgtgtaactgacttttctcga-taagtaaattagtaaaatacagaggacttctcactgagaaaaccattttt--ttgttta----tgactttatgt---agCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G02440.1 (Glycine max), 3'ss of exon 1
cgattcatt-agctcccgaagacta---agaggatttgtggacttagaagccagcttgatgatccatggatctctgattattcagtgttgatgttatgt-tgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
||| ||| || || | || | | |||| | | | ||| || || ||| | | | ||| || | || | || | | | |||||||||| || || || | |||||| | | | |||||||| ||| ||||| ||||| ||||| |||||||||||||| ||| | || || || || |
aaatttattgagaattacaaaattataaataaaatttattaaatatgaaaagag-----tgccacatatttttgtaatttttaacaattttttttgtttatatagCTTAACATTGTAGAGGGCATGATGCAACATCTATTTGATGAGAATGGCAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATTTCTTGTGGACATT
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 1
cgattcattagctcccgaagactaagaggatttgtggacttagaa-gccagcttgatg--atccatggatctctgat-tattcagtgttgatgttatgt-tgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
|||| | || | | || || || || ||| || | || | || |||| || | | | ||| || |||||| ||| | || | |||||||||||||||||||| |||| |||||||| ||| | ||| ||||| |||||||||||||||||||| |||||||| || || || |
---atcataaact--aatatatgaacagacttgatgtactcagtacacctaataaatatcatcccaacattgcatacatgttctaacttttcattatgtacacagGTCAATGTTGTTGAAGGGAAGATGCAGTATTTGTTTGATGAGAATGGCAAGCGCTATCTTGATGCCTTTGCTGGAATAGTTACTGTGTCATGTGGGCATT
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S32_198V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------cgattcattag-ctcccgaagactaagaggatttgtggacttagaag--ccagcttgatgatccatggatct-ctgattatt----cagtgttgatgttatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
| ||||| | | | || || || ||| ||| | || ||| ||||| | | | ||||| | || |||| || |||||||| || || || ||||| |||||||||||| ||| ||||||||||||| |||| || |||| ||||| || || || || || ||||| || ||
gtaggtttagacactctcttgaataatgcaatgcgttacttcattttgtataaatggtgtttcaggtgctgcaaattaggtttctgcaggggtagcctcttgtgggagagagacggtccggctc--tgatcagagtttatactgatggtagaagcaccattgacgtggcattgcagCTGAATATTGTGGAAGGAAAGATGCAGTACCTGTTTGATGAGAGTGGTCGGCGCTACTTGGACGCCTTCGCAGGCATTGTGACAGTGTCTGTAGGCCATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116444401|gb|EG486993.1|EG486993EST: AACGGAAGAAGTTTCTCGGACCTTCTCTTTTCCACTACTACCAGAAGCCT CTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGG
genomic: AACGGAAGAAGTTTCTCGGACCTTCTCTTTTCCACTACTACCAGAAGCCTgtacgtccgt ... tatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccagcttgatgatccatggatctctgattattcagtgttgatgttatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
tgttgat putative branch site (score: 4)
tgattatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgattcattagctcccgaagactaagaggatttgtggacttagaagccagcttgatgatccatggatctctgattattcagtgttgatgttatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - agactaa
- - - - - - - - - - - - - - gatttgt
- - - - - - - - - - - - - - - - - - - - - gaagcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgga